[gmx-users] Umbrella Sampling Tutorial Question

[Agnivo Gosai]

Dear Users

Firstly thanks to Dr. Lemkul for his immensely informative and helpful
tutorials. I am following the umbrella sampling tutorial for one of my
projects.
During the placement of the molecule inside the box , the tutorial tells us
to visualize in VMD. Now , upon visualizing I find that the 4 strands of
protofibril protein look separated.
Then we are to restrain one of the strands and pull the next stand in the
pulling simulation.
I can not understand how this is physically possible as the strands
"appear" to be "physically separated" and we proceed to calculate PMF based
on binding energy.

Kindly shed some light on this issue , please. Pardon for my ignorance.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.